My 12 year old is questioning everything about church

Son came home asking why God lets bad things happen and why he has to go to youth group if he doesn't believe in half of it. Instead of shutting him down I actually sat with him and we talked for two hours. I told him my faith journey has questions too and that's okay. Anyone else had this phase with their kids? I want to lead them to faith but not force it. Starting to think this conversation was a blessing in disguise.